Add descriptions PICRUSt2‐MPGA database

This page has been modified from the original Add descriptions page. You can see full details on the updates made to the PICRUSt2 database here.

add_descriptions.py is a convenience script that will add a column to your table of gene family or pathway abundances corresponding to a quick description of each functional category. These descriptions are in picrust2/default_files/description_mapfiles. You can also use custom mapping files.

The only update to this script from the previous add_descriptions.py script (details here) is the location of the reference files.

To add a description column to E.C. number, KO, and MetaCyc pathway abundance tables respectively:

add_descriptions.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC \
                    -o EC_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

add_descriptions.py -i KO_metagenome_out/pred_metagenome_unstrat.tsv.gz -m KO \
                    -o KO_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

add_descriptions.py -i pathways_out/path_abun_unstrat.tsv.gz -m METACYC \
                    -o pathways_out/path_abun_unstrat_descrip.tsv.gz

Arguments/options:

• -i: Input function abundance table.
• -o: Output function abundance table with added description column.
• -m: Mapping table to use (if one of the default tables should be used).
• --custom_map_table: Custom mapfile to use if using a non-default function database.